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  5. Whole-genome sequencing
  7. Somatic SNV detection
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OMIC
00092

SomaticSniper

The purpose of this program is to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files).

Specifications

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS
Programming languages:
C
Computer skills:
Advanced
Stability:
Stable
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Publications

  • (Larson et al., 2012) SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics.
    PMID: 22155872

Classification

Literature

  • (Spencer et al., 2014) Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. The Journal of molecular diagnostics.
    PMID: 24211364
  • (Stead et al., 2013) Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution. Human mutation.
    PMID: 23766071
  • (Roberts et al., 2013) A comparative analysis of algorithms for somatic SNV detection in cancer. Bioinformatics.
    PMID: 23842810
  • (Wang et al., 2013) Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome medicine.
    PMID: 24112718

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